There are 26 natural lakes and small lakelets, which were formed during a post-glacial period in the Park. Their total area is 1484.2 ha. Three largest lakes, Lake Plateliai, lake Ilgis and Beržoras lake, occupy approximately 90% of the total area. The bottom relief of these lakes is complex, and there are islands on all of them (Lake Plateliai has 7 islands, lake Ilgis has 2 ones and Beržoras lake has 1 island). The most picturesque, the cleanest and deepest lake in the Park and in Žemaitija region is Lake Plateliai. Its area is 1205 ha, the average depth –10.5 m, the deepest point – 50 m, the average water level –146.5 m above sea level.
There are lots of small lakes in the territory of the Park, 23 of them have the area less than 5 ha each; and another 10 natural water reseroirs have the area less than 1 ha each.
The lakes of Burgis and Luoka have vegetation of Chara spp. The lakes of Burgis, Burgalis and Skyplaičiai have lots of benthic vegetation of Chara spp. Acoording to the EU Directive on vegitations the above lakes may be defined as a hard oligo-mesotrophic waters with the benthic vegetation of the Chara spp.The lakes of Vaivadė (Petreikis), Burgis, Endriuškaičiai, especially their turfy bays are full of Magnopotamion and Hydrocharition. There are lots of natural nourishment in these lakes, they are natural eutrophic lakes with Magnopotamion or Hydrocharition-type vegetation. There are small lakes surrounded by marsh in the Park (Lestis, Piktežeris, Aklaežeris), thery are attributed to natural dystrophic lakes. There is almost no flora in them; the water is brown because of turf and humus accids.